Contacts of the helix formed by residues 239 - 257 (chain C) in PDB entry 3OP5
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 239 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C VAL* 3.5 16.8 - - - +
204C TYR* 4.6 3.1 - - - -
210C HIS* 3.8 16.8 - - - -
231C ASP* 4.2 2.5 + - - -
237C ALA 3.6 1.0 + - - -
238C PRO* 1.3 74.9 - - - +
240C ARG* 1.3 65.2 + - - +
241C ARG* 3.4 12.4 - - - +
242C GLY* 3.3 12.6 + - - +
243C ASP* 3.5 7.6 + - - +
311C TYR* 2.8 50.9 + - - -
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Residues in contact with ARG 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C HIS* 3.5 32.1 - - + +
170C GLU* 4.5 7.7 + - - -
174C VAL* 3.7 1.1 - - - +
204C TYR* 3.2 40.0 + - + -
205C CYS* 5.5 3.0 - - - -
210C HIS* 3.8 13.1 + - - -
239C SER* 1.3 75.5 - - - +
241C ARG* 1.4 62.6 + - - +
243C ASP* 3.2 15.4 + - - +
244C LEU* 3.4 16.9 + - - +
311C TYR 4.8 1.3 + - - +
312C THR 3.0 27.1 + - - -
313C GLU 3.7 6.6 + - - +
314C LYS* 3.5 41.0 - - - +
315C PRO* 3.7 14.6 - - + -
317C TYR* 3.5 16.1 + - - -
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Residues in contact with ARG 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C TYR* 4.2 8.3 + - - -
231C ASP* 2.8 39.2 + - - +
239C SER* 3.8 8.9 + - - +
240C ARG* 1.4 76.1 - - - +
242C GLY* 1.3 60.4 + - - +
244C LEU* 3.3 4.7 + - - +
245C GLU* 2.9 29.7 + - - +
279C ARG* 4.4 6.1 - - - +
306C VAL* 3.7 8.4 - - + +
309C LEU* 3.0 60.5 + - + +
310C ASP* 3.5 15.3 + - - +
311C TYR* 3.4 27.3 + - - +
313C GLU 5.3 2.0 + - - +
315C PRO* 5.0 0.2 - - - +
366C EDO 3.7 28.2 + - - +
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Residues in contact with GLY 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C SER* 3.7 23.2 - - - -
231C ASP* 4.6 3.1 + - - -
238C PRO* 6.0 2.5 - - - -
239C SER* 3.3 11.8 + - - -
240C ARG 3.2 1.2 - - - -
241C ARG* 1.3 82.4 - - - +
243C ASP* 1.3 56.0 + - - +
245C GLU* 3.2 4.8 + - - +
246C ILE* 2.9 38.8 + - - +
366C EDO 4.4 4.5 - - - -
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Residues in contact with ASP 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C LEU* 3.6 14.0 - - + +
169C HIS* 2.7 30.8 + - + +
174C VAL* 3.5 10.3 - - - +
175C HIS 2.9 22.1 + - - -
176C GLY* 2.8 30.9 + - - -
178C ILE* 3.6 24.4 - - + +
238C PRO* 5.4 0.9 - - - +
239C SER 3.5 2.7 + - - +
240C ARG 3.2 9.9 + - - +
242C GLY* 1.3 74.4 - - - +
244C LEU* 1.3 57.1 + - - +
246C ILE* 3.6 1.7 + - - -
247C LEU* 3.2 23.2 + - - +
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Residues in contact with LEU 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C LEU* 3.7 29.6 - - + -
165C LEU* 4.0 14.8 - - + -
169C HIS* 4.9 2.2 - - + -
240C ARG 3.4 9.4 + - - +
241C ARG 3.3 7.3 + - - +
242C GLY 3.3 0.4 - - - -
243C ASP* 1.3 72.4 - - - +
245C GLU* 1.3 60.0 + - - +
247C LEU* 3.5 1.0 + - - -
248C GLY 3.1 15.6 + - - -
302C TYR* 2.6 30.2 + - - +
306C VAL* 3.8 12.6 - - + -
309C LEU* 3.8 14.4 - - + -
315C PRO* 3.6 37.5 - - + -
317C TYR* 4.7 10.3 - - + -
320C LEU* 3.7 15.3 - - + -
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Residues in contact with GLU 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C SER* 3.6 4.8 - - - -
230C ILE* 3.2 28.6 + - - +
241C ARG 2.9 12.8 + - - +
242C GLY 3.4 8.7 - - - +
244C LEU* 1.3 73.4 - - - +
246C ILE* 1.4 64.6 + - - +
248C GLY* 3.0 12.8 + - - -
249C TYR* 2.6 53.1 + - + +
279C ARG* 5.8 1.6 - - - -
302C TYR* 5.4 0.4 - - - -
303C MET* 5.0 6.3 - - + +
306C VAL* 3.9 13.4 - - + +
366C EDO 2.5 39.1 + - - -
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Residues in contact with ILE 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C GLY* 3.6 38.6 - - - +
177C ASP* 4.2 1.3 - - - +
178C ILE* 3.1 40.6 - - + +
227C PHE* 3.2 32.0 - - + +
228C THR* 4.1 3.8 - - - +
229C SER* 3.8 19.5 - - - +
242C GLY 2.9 27.1 + - - +
243C ASP* 3.7 7.9 - - - +
245C GLU* 1.4 75.2 - - - +
247C LEU* 1.4 61.4 + - - +
249C TYR* 3.2 5.9 + - - +
250C CYS* 3.0 21.3 + - - -
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Residues in contact with LEU 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C SER* 3.9 26.9 - - - +
161C ILE* 3.8 45.1 - - + -
162C LEU* 3.9 22.4 - - + -
165C LEU* 4.5 6.3 - - + -
178C ILE* 4.8 6.5 - - + +
243C ASP 3.2 14.4 + - - +
244C LEU* 3.6 1.8 - - - +
245C GLU 3.3 0.2 - - - -
246C ILE* 1.4 75.3 - - - +
248C GLY* 1.3 55.8 + - - +
250C CYS* 3.2 9.1 + - + +
251C MET* 2.9 40.0 + - + +
254C TRP* 4.5 8.7 - - + -
302C TYR* 3.6 24.2 - - + +
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Residues in contact with GLY 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C LEU 3.1 7.1 + - - -
245C GLU 3.0 8.9 + - - -
247C LEU* 1.3 73.5 - - - +
249C TYR* 1.4 59.9 + - - +
251C MET* 3.3 13.6 + - - +
252C ILE* 3.3 25.6 + - - +
299C ILE* 5.3 0.3 - - - +
302C TYR* 3.7 21.0 - - - -
303C MET* 3.8 16.8 - - - +
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Residues in contact with TYR 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C PHE* 3.3 36.1 - - + -
228C THR 3.5 15.3 - - - -
230C ILE* 4.1 4.3 - - - +
245C GLU* 2.6 49.4 + - + +
246C ILE 3.2 5.1 + - - +
248C GLY* 1.4 71.4 - - - +
250C CYS* 1.3 59.3 + - - +
252C ILE* 3.4 4.9 + - + +
253C GLN* 3.0 29.0 + - - +
259C LEU* 3.5 18.5 - - + +
261C TRP* 3.6 26.2 - + - -
275C LYS* 3.5 32.8 + - + +
278C TYR* 6.4 0.7 - - + -
279C ARG* 5.5 1.7 - - - +
285C LEU* 5.3 2.2 - - + -
303C MET* 3.8 24.5 - - + -
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Residues in contact with CYS 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C ILE* 3.3 32.1 - - - -
179C LYS* 3.8 15.5 - - - -
227C PHE* 4.2 15.9 - - - -
246C ILE 3.0 16.4 + - - +
247C LEU* 3.3 13.0 - - + +
249C TYR* 1.3 75.0 - - - +
251C MET* 1.4 51.4 + - - +
253C GLN* 3.3 7.0 + - - +
254C TRP* 2.9 66.7 + - + +
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Residues in contact with MET 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C VAL* 3.8 17.5 - - + -
155C LEU* 5.8 0.7 - - - -
158C SER* 3.2 35.4 - - - +
247C LEU* 2.9 20.4 + - + +
248C GLY* 3.3 13.0 + - - +
250C CYS* 1.4 74.6 - - - +
252C ILE* 1.4 56.6 + - + +
254C TRP* 3.4 5.8 + - + +
255C LEU* 3.0 37.2 + - - +
299C ILE* 3.9 31.2 - - + -
302C TYR* 3.5 46.0 - - + -
324C LEU* 4.2 11.0 - - + -
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Residues in contact with ILE 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C GLY 3.3 15.0 + - - +
249C TYR* 3.8 11.4 - - + +
251C MET* 1.4 71.2 - - - +
253C GLN* 1.3 55.6 + - - +
255C LEU* 3.3 5.1 + - - -
256C THR* 2.8 43.0 + - + +
258C HIS 3.9 5.8 - - - +
259C LEU* 3.8 14.4 - - + -
260C PRO* 5.3 0.2 - - + -
285C LEU* 3.8 32.1 - - + -
286C MET* 4.2 9.9 - - + -
289C CYS* 3.6 32.1 - - + -
290C PHE* 4.4 9.2 - - + -
299C ILE* 4.0 19.3 - - + -
303C MET* 4.1 11.7 - - + -
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Residues in contact with GLN 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C TYR* 2.8 50.2 + - + +
147C LYS* 5.5 2.6 - - - +
226C GLU* 5.4 1.6 - - - +
227C PHE* 3.8 27.7 - - + -
249C TYR 3.0 16.9 + - - +
250C CYS 3.5 4.0 - - - +
252C ILE* 1.3 75.1 - - - +
254C TRP* 1.3 62.0 + - + +
257C GLY* 2.8 35.6 + - - -
258C HIS* 3.6 15.8 + - - +
259C LEU* 3.5 25.8 + - + +
262C GLU* 4.3 5.8 + - - +
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Residues in contact with TRP 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C LEU* 5.0 2.0 - - + -
142C TYR* 3.7 21.8 - + - -
147C LYS 4.4 0.2 - - - +
148C ARG* 3.5 7.1 - - - -
149C PHE* 2.9 47.4 + + + -
154C VAL* 3.7 22.4 - - + -
157C LEU* 4.1 26.2 - - + -
158C SER* 4.5 9.0 - - - -
161C ILE* 3.8 17.0 - - + -
178C ILE* 5.5 0.4 - - + -
180C ALA* 3.8 29.2 - - + +
183C LEU* 3.7 32.1 - - + -
227C PHE* 5.9 2.4 - - - -
247C LEU* 4.5 3.8 - - + -
250C CYS* 2.9 50.6 + - + +
251C MET* 3.8 7.0 - - - +
253C GLN* 1.3 84.2 - - + +
255C LEU* 1.3 61.4 + - - +
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Residues in contact with LEU 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C ARG* 3.7 12.4 - - - -
149C PHE 4.0 7.9 - - - +
151C ARG* 3.7 39.5 - - + +
154C VAL* 3.8 17.7 - - + -
251C MET 3.0 21.6 + - - +
252C ILE 3.8 3.1 - - - +
254C TRP* 1.3 78.5 - - - +
256C THR* 1.3 57.3 + - - +
290C PHE* 4.1 23.2 - - + -
296C PRO* 4.2 8.7 - - + -
298C GLU* 5.9 0.2 - - - +
299C ILE* 3.8 35.0 - - + -
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Residues in contact with THR 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ARG* 3.1 24.1 + - - +
252C ILE* 2.8 26.2 + - - +
255C LEU* 1.3 73.0 - - - +
257C GLY* 1.3 56.7 + - - +
258C HIS* 2.9 38.0 + - - +
289C CYS* 3.3 33.8 - - + +
290C PHE* 3.5 31.4 - - + -
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Residues in contact with GLY 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C TYR* 3.3 3.2 + - - -
147C LYS* 3.2 33.2 + - - +
148C ARG* 3.4 7.0 + - - -
253C GLN* 2.8 35.3 + - - -
255C LEU 3.8 1.0 - - - -
256C THR* 1.3 69.7 - - - +
258C HIS* 1.4 74.7 + - - +
262C GLU* 4.2 1.7 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il